Sequence
atgc intronic sequence ATGC exonic sequenceCCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta...
Basic information
species | Glycine max |
transcript | GLYMA13G39270.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta
|| ||||||||| | || || || ||||| || |||||||| ||||| | || |||||||||||||| |||||||| |||||||||||||| || ||||| || | ||| || | | | || || ||| | || | ||| || | | | | || | |
TCAAAAGGACAAGAGATTTAGCGGTTCTGTGAAATTGCCTCACGTTCCTAGGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgtt-cacttttttccgccttttcttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggttggtt-tacttag------------
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta
|| ||||| |||||||||||||| ||||| ||| | || |||||||||||||| || |||||||| ||||||||||||||||| ||||| ||||||||||| | ||| | | || | | | || || || | | | || | || ||| | |||
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctat--------actttttgtgtatcttgtttggtttgaattggtgattgacacaaagtgtttgatgtttgttttgatag-------
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 5'ss of exon 3
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta--
|| |||||||||||||||||||| ||||| ||||| || ||||| || || || || |||||||| || ||||| |||||||||||||| ||||| ||||| | | ||| | | | || | | | || | | || | | | || |||| | | | || | | ||
TCAAAAGGACAAGCGTTTCAGTGGATCTGTCAAGTTACCACATATCCCCCGTCCTAAAATGAAGATCTGCATGCTCGGAGATGCCCAGCATGTTGAAGAGgtgatatatcttttcatggaaattgatcattttgtgctct-gtttcttgtataatggttttgtgctcatttcatttggtggc-tctattagtttcatttgat
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 5
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttac-attagataacacctgggatgtatgctta-
|||||||||||||||||||||||| ||||| |||||||| || || |||||||||||||||||| | || |||||||| ||||| || ||||| || ||||||| | | | || | | | | | || ||| | | || | | || || | | || | || || | | || |||
CCAGAAGGACAAGCGTTTCAGTGGTTCTGTGAAGTTGCCCCACATCCCTCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCTCAACACGTGGAAGAGgtaattgtgctccac-ttggctgcattaatggcaataaaagaagtgaaagacaagtgtcattgctaattgaagaatatttttcaactatttttt-tgtttaa
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagatt-caatcgtgtgcttcattgttttcctagat--attttacattagataacacctgggatgtatgctta---
|||||| ||||| |||||||| |||||||| ||| |||| || |||||||| || ||||||| | || |||||||||||||| |||||||| |||||||| | | | | || | | | | | | || | || | | || || ||| || | |||| |||| | | | || |
CCAGAAAGACAAACGTTTCAGCGGCTCTGTGAAGCTGCCACACATTCCTCGTCCTAAGATGAGAGTGTGCATGCTTGGAGATGCTCAGCACGTCGAGGAGgtcatattcg--cacattggaataatttttgccttcatatttgtttcatttttagattatcttgattaatgtctcatttcttaac-caacgttcatctgacaatag
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagat-tcaatcgtgtgcttcattg-------ttttcctagatattttacattagataacacctgg--gatgtatgctta-----------------------------------------------------------------------------------
|||||| |||||||||||||||||||| || ||| | || || |||||||| || ||||||| |||||||||||||||||||||||| || |||| |||||| || | | | | || | | | | || ||| |||| || || || | | | | | || || | | || ||
CCAGAAAGACAAGCGTTTCAGTGGCTCCGTGAAGCTTCCCCACATTCCTCGTCCTAAGATGAGGATTTGTATGCTTGGAGATGCCCAACATATTGAAGAGgtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacag
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 5'ss of exon 2
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgta--------acaataatttatgctgtagagaaccacgag-attcaatc-gtgtgcttcattgttttcctagat-attttacattagataacacctgggatgtatgctta
|||||| ||||||||||||||||| || || ||| |||| || ||||||||||| |||||| | || ||||| ||||||||||||||||||||||||||| | || | |||| | | || ||| || | ||| |||| | ||| | | ||| | | || || |
CCAGAAAGACAAGCGTTTCAGTGGTTCCGTGAAGCTGCCACACATTCCTCGCCCTAAGATGCGCGTGTGCATGCTCGGAGATGCCCAGCACGTTGAGGAGgtatttcctctaactcaactaatgccacccatgttgagaagcattttgtcagcatgccacattacgcaggttgattacctcttatttattcgccccattattgcgtaacag
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatt--tatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta
|||||||||||||||||||| ||||| || ||| ||||||| ||| | || |||||||||| | || ||||| || ||||| ||||| || | ||||||| | | | | | | |||| |||| || | ||||| ||| | | |
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaagattgagcgccctctctcctttagttgccggattgaatcac-tggtccattgcttttttgcacag---------------------------------
upper sequence: GLYMA13G39270.2 (Glycine max), 5'ss of exon 2
lower sequence: EFJ34353 (Selaginella moellendorffii), 5'ss of exon 2
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatt--tatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctag-atattttacattagataacacctgggatgtatgctta
|||||||||||||||||||| ||||| || ||| ||||||| ||| | || |||||||||| | || ||||| || ||||| ||||| || | |||||||| | | | || | |||| |||| || | | ||| ||| | | | |
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCCCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGGGAGgtaagattgagcgccctgtctccttttgttgccggattgaatcac-tggtccgttgctttttttgcacag---------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|207694943|gb|GD676690.1|GD676690EST: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAG GCTGAGAAGATAGGATTGGACTACATGGATGTTGAGG
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataa ... ggatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTTGAGG
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCAGAAGGACAAGCGTTTCAGTGGCTCTGTTAAGTTGCCTCATATTCCTCGCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAGCACGTTGAGGAGgtaacaataatttatgctgtagagaaccacgagattcaatcgtgtgcttcattgttttcctagatattttacattagataacacctgggatgtatgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG